libhdf5.so

[Andrey Brukhno]

Hello,

Upon a successful installation of the VOTCA's development (master) branch I get this error:

~/votca-dev/bin/csg_map

/home/andrey/votca-dev/bin/csg_map: error while loading shared libraries: libvotca_csg.so.5: cannot open shared object file: No such file or directory

I tried to reinstall libhdf5-dev twice, also checked for all the other dependencies, everything looks fine, yet the error.

Meanwhile the 'stable' branch (1.4.1 apparently) did install correctly and appears to work. 

Would appreciate any clues or a fix.

Thanks

Andrey

PS: for reference, below is the output messages from cmake for my attempted installation of 'master'

build > cmake -DBUILD_CSGAPPS=ON -DBUILD_TOOLS=ON -DWITH_GMX=ON -DWITH_SQLITE3=OFF -DCMAKE_INSTALL_PREFIX=$HOME/votca-dev ..

-- Boost version: 1.58.0

-- Found the following Boost libraries:

--   program_options

--   filesystem

--   system

-- Intel(R) MKL could not be found.

-- Boost version: 1.58.0

-- Found the following Boost libraries:

--   program_options

--   filesystem

--   system

-- Intel(R) MKL could not be found.

-- Checking for module 'libgromacs_d'

--   No package 'libgromacs_d' found

-- Could NOT find GMX (missing:  GMX_EXECUTABLE) 

-- Boost version: 1.58.0

-- Found the following Boost libraries:

--   program_options

-- Intel(R) MKL could not be found.

-- Could NOT find CLANG_FORMAT (missing:  CLANG_FORMAT_EXECUTABLE) 

-- 

-- The following OPTIONAL packages have been found:

 * Git

 * FFTW3

 * EXPAT

 * TXT2TAGS

 * UnixCommands

 * HDF5

 * Eigen3

 * PkgConfig

 * Doxygen

-- The following REQUIRED packages have been found:

 * Threads

 * GROMACS (required version >= 20160000)

 * Boost (required version >= 1.57.0)

 * EIGEN3 (required version >= 3.3.0)

 * VOTCA_TOOLS

 * VOTCA_CSG

-- The following OPTIONAL packages have not been found:

 * MKL

-- Configuring done

-- Generating done

CMake Warning:

  Manually-specified variables were not used by the project:

    BUILD_TOOLS

-- Build files have been written to: /home/andrey/Progs/votca-dev/votca-1.5-master/build

[bg:0](st:0) andrey@AndysHome: build > make 

...

[Christoph Junghans]

On Fri, Sep 7, 2018 at 11:03 AM 'Andrey Brukhno' via votca
<vo...@googlegroups.com> wrote:
>
> Hello,
>
> Upon a successful installation of the VOTCA's development (master) branch I get this error:
>
> ~/votca-dev/bin/csg_map
> /home/andrey/votca-dev/bin/csg_map: error while loading shared libraries: libvotca_csg.so.5: cannot open shared object file: No such file or directory

That just means you have to source VOTCARC.bash

We also recently added the option to inject an rpath on Linux, i.e.
-DENABLE_RPATH_INJECT=ON, then the location of libvotca_csg.so.5 will
be stored in csg_map itself.

>
> I tried to reinstall libhdf5-dev twice, also checked for all the other dependencies, everything looks fine, yet the error.

Not sure how this related to libhdf5, the above error refers to
libvotca_csg.so.5, right?

>
> Meanwhile the 'stable' branch (1.4.1 apparently) did install correctly and appears to work.
>
> Would appreciate any clues or a fix.
>
> Thanks
> Andrey
>
> PS: for reference, below is the output messages from cmake for my attempted installation of 'master'
>
> build > cmake -DBUILD_CSGAPPS=ON -DBUILD_TOOLS=ON -DWITH_GMX=ON -DWITH_SQLITE3=OFF -DCMAKE_INSTALL_PREFIX=$HOME/votca-dev ..

And yeah there is no BUILD_TOOLS option.

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--
Christoph Junghans
Web: http://www.compphys.de

[Andrey Brukhno]

Hi Christoph, thanks for your response.

On Friday, September 7, 2018 at 7:05:28 PM UTC+1, Christoph Junghans wrote:

On Fri, Sep 7, 2018 at 11:03 AM 'Andrey Brukhno' via votca
<vo...@googlegroups.com> wrote:
>
> Hello,
>
> Upon a successful installation of the VOTCA's development (master) branch I get this error:
>
> ~/votca-dev/bin/csg_map
> /home/andrey/votca-dev/bin/csg_map: error while loading shared libraries: libvotca_csg.so.5: cannot open shared object file: No such file or directory
That just means you have to source VOTCARC.bash

Yes, sorry I missed to include that from my terminal output (I meant to show that resulting error):

---

build > ~/votca-dev/bin/csg_map

/home/andrey/votca-dev/bin/csg_map: error while loading shared libraries: libvotca_csg.so.5: cannot open shared object file: No such file or directory

build > . ~/votca-dev/bin/VOTCARC.bash 

build > ~/votca-dev/bin/csg_map

/home/andrey/votca-dev/bin/csg_map: error while loading shared libraries: libhdf5.so.101: cannot open shared object file: No such file or directory

---

Note that I tried to install the 'master' twice, repeating the entire process, starting with "git clone -b master ...", both times I ended up with the above error message about missing libhdf5.so.101, whereas it was installed and the installation of 'stable' branch did not complain at all.

We also recently added the option to inject an rpath on Linux, i.e.
-DENABLE_RPATH_INJECT=ON, then the location of libvotca_csg.so.5 will
be stored in csg_map itself.

What does it help? (before it seemed to work fine without it)

 

>
> I tried to reinstall libhdf5-dev twice, also checked for all the other dependencies, everything looks fine, yet the error.
Not sure how this related to libhdf5, the above error refers to
libvotca_csg.so.5, right?

>
> Meanwhile the 'stable' branch (1.4.1 apparently) did install correctly and appears to work.
>
> Would appreciate any clues or a fix.
>
> Thanks
> Andrey
>
> PS: for reference, below is the output messages from cmake for my attempted installation of 'master'
>
> build > cmake -DBUILD_CSGAPPS=ON -DBUILD_TOOLS=ON -DWITH_GMX=ON -DWITH_SQLITE3=OFF -DCMAKE_INSTALL_PREFIX=$HOME/votca-dev ..
And yeah there is no BUILD_TOOLS option.

Okay, I noticed. I think including it did not affect anything (?).

Andrey

[Andrey Brukhno]

Just to make sure, I have done it for the third time now, with the same result (error about libhdf5).

This is strange because the camke log reports it as found:

$ grep HDF master-cmake.log

-- Found HDF5: /home/andrey/anaconda2/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/andrey/anaconda2/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.1") 

 * HDF5

whereas the 'stable' branch does not require it, apparently; at least cmake does not report anything about libhdf5.

Andrey

[Christoph Junghans]

On Sat, Sep 8, 2018, 09:43 'Andrey Brukhno' via votca <vo...@googlegroups.com> wrote:

Just to make sure, I have done it for the third time now, with the same result (error about libhdf5).

This is strange because the camke log reports it as found:

$ grep HDF master-cmake.log

-- Found HDF5: /home/andrey/anaconda2/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/andrey/anaconda2/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.1") 

 * HDF5

whereas the 'stable' branch does not require it, apparently; at least cmake does not report anything about libhdf5.

Yeah, in the stable branch the hdf5 I/O backend is off by default, while it gets enabled automatically in master when an HDF5 library is found! The code has matured enough since it was added in 1.4!

There error is due to the fact that your libhdf5 is in non-common place and hence LD cannot find it at runtime! Either add that directory to your LD_LIBRARY_PATH or try the new inject rpath option in master. Or you could also disable the HDF5 backend if you don't need it.

Christoph

[Andrey Brukhno]

The question is, what is the significance of this library (libhdf5)? - from what you say I gather, it is not required in general, but it is only necessary if I myself indent to use hdf5 files/data (which obviously I am not currently; unless it is used by VOTCA tools or scripts somewhere under the hood - ?).

Anyway, what is the cmake option to switch it off (I could not find it)?

Thanks

Andrey

[Christoph Junghans]

On Sat, Sep 8, 2018 at 11:24 'Andrey Brukhno' via votca <vo...@googlegroups.com> wrote:

The question is, what is the significance of this library (libhdf5)? - from what you say I gather, it is not required in general, but it is only necessary if I myself indent to use hdf5 files/data (which obviously I am not currently; unless it is used by VOTCA tools or scripts somewhere under the hood - ?).

HDF5 is used to read H5MD files!

Anyway, what is the cmake option to switch it off (I could not find it)?

-DCMAKE_DISABLE_FIND_PACKAGE_HDF5=ON

Christoph 

[Andrey Brukhno]

On Saturday, September 8, 2018 at 6:42:03 PM UTC+1, Christoph Junghans wrote:

On Sat, Sep 8, 2018 at 11:24 'Andrey Brukhno' via votca <vo...@googlegroups.com> wrote:

The question is, what is the significance of this library (libhdf5)? - from what you say I gather, it is not required in general, but it is only necessary if I myself indent to use hdf5 files/data (which obviously I am not currently; unless it is used by VOTCA tools or scripts somewhere under the hood - ?).

HDF5 is used to read H5MD files!

Alright, whatever.. I suppose it is from here: https://support.hdfgroup.org/HDF5/Tutor/

 

Anyway, what is the cmake option to switch it off (I could not find it)?

-DCMAKE_DISABLE_FIND_PACKAGE_HDF5=ON

OK, thanks a lot!

Just for completeness, I did try to update my LD_LIBRARY_PATH including both standard and non-standard locations for the related lib files. However, I still see the following in the cmake report, where I flagged all the supposedly relevant lines with triple asterisk ***

...

-- Found HDF5: /home/andrey/anaconda2/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/andrey/anaconda2/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.1")  ***

-- Could NOT find GMX (missing:  GMX_EXECUTABLE) 

-- Boost version: 1.58.0

-- Found the following Boost libraries:

--   program_options

-- Checking for module 'libvotca_tools'

--   No package 'libvotca_tools' found

-- Intel(R) MKL could not be found.

-- Checking for module 'libvotca_csg'

--   No package 'libvotca_csg' found

-- Found VOTCA_CSG: votca_csg  

-- Could NOT find CLANG_FORMAT (missing:  CLANG_FORMAT_EXECUTABLE) ***

-- 

-- The following OPTIONAL packages have been found:

 * Git

 * FFTW3

 * EXPAT

 * TXT2TAGS

 * UnixCommands

 * HDF5 ***

 * Eigen3

 * PkgConfig

 * Doxygen

---

I have two questions regarding the above.

1. Is the line complaining about not found CLANG_FORMAT related in any way to the libhdf5?

2. Can it be that at the building time the libraries from different sources are confused or mixed up somehow upon linking? (so that at run time a wrong library is searched for)

Andrey

[Andrey Brukhno]

After all, it did work and now I get no error when I tried csg_call, csg_map, csg_stat or csg_reupdate etc.

However it did complain all the way during installation:

cmake: /home/andrey/anaconda2/lib/libssl.so.1.0.0: no version information available (required by /usr/lib/x86_64-linux-gnu/libcurl.so.4)

cmake: /home/andrey/anaconda2/lib/libssl.so.1.0.0: no version information available (required by /usr/lib/x86_64-linux-gnu/libcurl.so.4)

cmake: /home/andrey/anaconda2/lib/libssl.so.1.0.0: no version information available (required by /usr/lib/x86_64-linux-gnu/libcurl.so.4)

cmake: /home/andrey/anaconda2/lib/libcrypto.so.1.0.0: no version information available (required by /usr/lib/x86_64-linux-gnu/libcurl.so.4)

Not sure how important it is though.

Thanks for your help!

Andrey

[Christoph Junghans]

No, that is just another things which didn’t get found, but it is also optional!

2. Can it be that at the building time the libraries from different sources are confused or mixed up somehow upon linking? (so that at run time a wrong library is searched for)

Not sure what you mean! CMake uses the libraries it detects for building and linking. However, once you install things the Linux loader, ld, is in charge. You can check what it is trying to load by running: “ldd <some_binary>”.

For csg_map that will show a missing libhdf5 in your case. LD_LIBRARY_PATH is just a way to help ld find stuff.

Christoph 

[Andrey Brukhno]

OK! After reading a bit about HDF5 data objects I thought CLANG_FORMAT might be an attribute in some data structure or container related to the C language.

 

2. Can it be that at the building time the libraries from different sources are confused or mixed up somehow upon linking? (so that at run time a wrong library is searched for)

Not sure what you mean! CMake uses the libraries it detects for building and linking. However, once you install things the Linux loader, ld, is in charge. You can check what it is trying to load by running: “ldd <some_binary>”.

For csg_map that will show a missing libhdf5 in your case. LD_LIBRARY_PATH is just a way to help ld find stuff.

I asked this question because merely adding my non-standard location for libhdf5.so (anaconda2/lib) to LD_LIBRARY_PATH did not resolve the issue. I had to rebuild and re-install the whole thing, and only then the error stopped popping up (which implies that it is not that simple as you describe).

Anyway it works now.

Andrey

[Christoph Junghans]

Cool, if you feel something needs to get added to installation guide, please propose a file change here:

https://github.com/votca/votca/blob/master/share/doc/INSTALL.md

Christoph 

[Andrey Brukhno]

I am not sure what you mean here: adding the description for the flag omitting hdf5? or the fact that one needs to add non-standard library locations to the LD_LIBRARY_PATH and then recompile everything?

Andrey

 

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